A Work In Progress
by Gleek-Whovianfangirl
Summary: Title may be changed. A SkyeWard multichapter fic loosely based on ideas from Clintasha. AU and rating may be changed. Team Bus members are still included. 'It had started seven years ago, Skye was a twenty year old on the run from several different organisations, her hacking had made her an asset everyone wanted on their side. She only worked independently.'
1. Chapter 1

**A/N I wanted to have a go at an Agents of Shield multi story fic so enjoy!**

 **I don't own anything!**

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It had started seven years ago, Skye was a twenty year old on the run from several different organisations, her hacking had made her an asset everyone wanted on their side. She worked independently, hence the reason she was on the run. That was until a twenty-three year old had made her a deal. She went with him, worked with him only and he'd make sure that all the other organisations would back off. So naturally she took the deal, part of the reason she took it could have been because she'd spotted the gun on his side and no one else had ever gotten this close to her, she didn't know how to handle herself in these situations.

She had stuck close to his side throughout the first few years, not talking to anyone or training with anyone else. She was only comfortable with the man she come to know as Grant Ward, her best friend who had nearly got himself killed by Director Fury for simply bringing her back to the Hub rather than the Fridge. Since then they'd become two of the handful of agents who never needed an extraction plan, no matter what the level of the mission was. Skye wasn't only the best hacker they had on the entire team but she was now also fully trained in combat and one of the best in level 7, thanks to her best friend.

Over time she had began to trust others that Ward said were okay including Agents Coulson, May and FitzSimmons but it was rare that she was the one to speak to the two older members, usually Ward did it. She gone on nine group missions with all them since she had joined Shield and had gotten into trouble some of those times for arguing against extraction teams, which of course they had to have as they weren't the only two on those missions. However, out of the four members of their team she considered herself to be close to the pair known as FitzSimmons, close enough that she practically considered them family.

Skye and Ward were nothing but extremely close friends regardless of what everyone else thought, she couldn't complain at the assumptions though, he was everyone's type. She had caught herself watching his muscles from the corner as he trained and when they went undercover as a couple, had often got quite into it but thankfully nothing came out of those missions once they'd debriefed. It was never brought up between them after that. Was she relieved about that? She wasn't too sure.

S&W S&W

"C'mon Skye. You always do this." He called through her bedroom as he knocked a little harder. "You've gotta get out of bed. Hill wants to see us about a mission." He told her and when he received a grunt from her, he knew it was okay to enter her room and he walked straight in. He had a key card because she never trusted herself on days like this and she knew that he'd only break down her door in order to get to her. "We've got a level 5 mission to go on, should be a piece of cake for us." He told her and walked over to her bed, perching on the edge of it as he pulled the covers down slightly so he could see her face. "Then once we're done you can come straight back up here and go back to sleep." He told her with a half smile as she opened one of her eyes to look at him.

"Level 5? Why do we have to go? Can't they send another pair in? Or are they just trying to get rid of us again." She laughed sleepily, before stretching an arm out over the covers to stretch slightly. She glanced over at the alarm clock by her bed. "It's 4am, how are you even fully awake at this time? We wouldn't even start training at this time back in the day." She mumbled to herself and sat up, the covers pulling at her waist. His top, that she'd acquired months ago, covered her fully. "It's gotta be real serious if we have to go at this time." She yawned before he smiled again and stood up.

"Sounds it. Want me to meet you down there or should I wait here?" He asked. "Because I'm sure going down in my shirt would only give them more reason to suggest we're together." He told her and nodded towards what she was wearing.

She shook her head. "You can wait here. I'll need someone to stop me just crawling back into bed once I'm ready to leave." She told him and got up too. She walked past him and went straight to the drawers opposite her bed, pulling out the black combats identical to Wards, only smaller. She made quick work of pulling the trousers on before quickly removing the shirt and pulling her black one on, tucking it in quickly, she wasn't worried about changes like this in front of him, he'd seen her in less while they were undercover and she knew that being the polite man he was he wouldn't be watching. "You also have to prevent me from being rude to whoever's in the room with Hill, you know how I can be on mornings." She smiled and quickly made her bed before walking over to him.

"I've experienced it multiple times, no need to remind me." He teased.

She hit his shoulder playfully. "That wasn't needed!" She told him before she grabbed his arm and pulled him from her room, shutting the door behind them both.

Throughout their briefing they'd been told that Skye needed to receive some information from three different computers in the building, the information being some planned Hydra attacks, it was only a high level mission because they were in a secure unit with at least two guards per door on the inside, more on the outside. They'd be travelling in with Coulson and their team as they had an unrelated lower level mission in that area.

Once they'd both gotten out the room Skye looked at him. "So we have two hours downtime till then." She paused. "Do you just want to go to the bus? We've got a few guns to choose from that I know Fitz has developed." She told him.

He just nodded. "I'll meet you there. I just need to go sort something out." He smiled before he walked away, leaving her no time to ask questions. She frowned before made her way to the hanger where the plane was kept.

S&W S&W

"You're back, Skye!" Fitz called from their onboard lab and sometimes medical room when needed. "We heard you were joining us but Coulson had a feeling you and Ward might just take off in a Quinjet for some reason."

"And leave someone I consider my little brother hanging? I'd never do that." She teased and made her way up to him, until she was stood on his left side. "You got any new toys I can take on this mission? By the sounds of it, I might end up needing them." Judging by the grin that had suddenly appeared on his face, she took that as a yes.

An hour and a half later Ward arrived exactly on the time they were meant to be leaving. He sent Skye and quick nod and a smile before disappearing up the spiral staircase to talk to Coulson, not that she knew that.

"Was that weird?" He asked Fitz and Simmons, the latter had joined them forty five minutes into weapons testing.

"That he arrived on time? No. Should it be?" Simmons asked and looked up from the microscope she was using.

"I meant that he didn't join us." She told them. "I'm sure he'll explain later." She shrugged with a smile but kept what had just happened in the back of her mind, it was probably nothing.

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 **So, hopefully if you guys like this (And tell me *Hint hint* ;) ) this will become a multi chapter. I'm kind of going in the direction of them being a bit like Clintasha but less you know, Avenger-y**

 **Also, this was more an introduction to set up my version of everything as it's gonna be AU.**


	2. Chapter 2

**Disclaimer: I don't own anyone or anything you recognise.**

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 **Chapter 2**

"So are we clear on what I'm asking you to do?" Ward asked Coulson slowly, trying to make him understand, which he had failed to do for the past hour and a half. "You extract her on my word and you'll all be safe. I promise you that." He repeated for what felt like the sixth time since he'd been in the room. "She asks any questions you think could be bad for her you don't answer." Ward told him.

Coulson nodded with a frown, still processing everything he'd been told by the younger Agent. "Got it. You know the chances of her accepting all of this are slim to none right?" He asked and leaned back in his leather chair. "I can't help you out of the mess you're creating. But I will keep her safe." He promised before opening the door from his desk.

"That's all I ask." He nodded before getting up, knowing that the opening of the door was his cue to leave. "Thank you sir." Was what he said as he was leaving, leaving Coulson on his own once more.

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"Well look who finally decided to show his face around here!" Skye called over to Ward as she saw him coming down the spiral staircase from Coulson's office. "Thought you'd left me again!" She teased before turning her cards when she realised Fitz was trying to see what she had. They were in the middle of an intense game of Go Fish and she didn't appreciate him trying to cheat. She'd won the last four games they'd played and he wasn't taking away her winning streak just yet.

"Leaving you was a one time thing and it stopped us both getting blown up. We met up a few hours later. It wasn't like I'd abandoned you forever, I mean I'd tried to but you're just too good at finding me apparently." He played along and walked over to her. Skye had gotten back into her game while he talked but he knew she was still listening.

"I'm going to ignore the fact you made a joke because it wasn't a nice one." She told him with a small smile. "Any five's?" She asked Fitz who just shook his head. From behind her Ward held up six fingers with a smirk directed towards the young engineer.

"Any sixes?" He asked and Skye frowned before handing over the three sixes she had in her hand.

She bit her lip when she saw Fitz not so discreetly wink at Ward, man he needed to work on his subtly skills. She dropped the cards face down before turning in her seat. "You didn't happen to have anything to do with that did you, Grant?" She asked. She only used his given name when she was being deadly serious or when she was playing with him, which often made it very hard for him, or anyone, to guess whether she was going to try attack them or just burst out laughing.

"Me? No I'd never do that to you." He shrugged casually but the look on his face said something completely different. "You know how much I love you winning at everything and putting everyone down when you do." He said sarcastically.

"I don't put people down, do I Fitz?" She asked and turned to him with a glare.

"No-I...You never do...well maybe sometimes." He stuttered, the almost deadly glare putting him off and made him stumble over his words.

She smirked at him. "You know I don't like cheaters but seeing as Ward is technically the cause of this all I'll just put the blame on him."

"I'm okay with that." Fitz replied before he put his cards down and quick walked back to the lab, away from them.

Skye frowned and looked at the cards that were now on the table. "Wanna play Go Fish? Looks like I've been ditched." She asked him, only to find him shaking his head.

"I'm off to start training. Need to feel fully prepared for this mission. I just have a bad feeling about what's going to go down." He admitted before he walked off.

"What are you talking about!" She called after him but didn't get a response from him.

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"Rumour has it that Garrett's still in the building." He mumbled to Skye. They'd already gotten into the building, which was surprisingly easier than either of them had anticipated. "If you see him, don't approach him. He's mine to take down." He mumbled his past with him was complicated to say the least, thanks to that man.

"I'll do what's needed but I'll keep that in mind." She whispered from beside him. "Don't lash out at him purely based on your past, you know I can't stop you from doing anything stupid once you start." She sighed, last time she'd tried to help it resulted in her getting her legs kicked out from underneath her, since then she'd found it easier for the both of them if she just stepped back when she knew the outburst that always followed.

Ward took out a man that came around the corner quickly with his gun, no icers. He needed Hydra dead, he wasn't going to go easy on any of them, Skye on the other hand only used icers, she didn't enjoy having blood on her hands, innocent or not.

"They know we're here." Ward told her and looked around the hallway for cameras, shooting one on his sweep around. "Why didn't we see any cameras on the sweep around the building from the Bus?" He asked her. "We found the computers from the Bus, how come we saw no cameras." He asked.

"They must have installed them after we'd done the scans, or they were deactivated during the scan." She replied. "Or they're the motion ones, only activate to movement. It would make them practically impossible to locate if people rarely came down here." She told him. She looked at the guard that had been shot down by her partner. "There should be more of them coming. We need to get moving Ward." She told him. As she finished her sentence the sound of heavy footsteps could be heard. "Or they've already realised we killed one of their own." She hissed before grabbing his arm. "Forget about the damn cameras, we need to get moving."

Ward pulled his arm away before he quickly led her down a hall that came off the one they were on. "You get to the computer, I'll get anyone who comes down this way. You only have two minutes max." He warned. Skye tried to open the door when they came to it but failed. Ward shot the lock twice before the handle came off. "Go." He muttered and turned back to face the hall again.

She jumped at the sound of gunshots but still copied everything onto the memory stick as quickly as she could, occasionally looking behind her to check the door had stayed shut. She turned around once she'd pulled the usb out and shoved it in her pocket. She instantly froze when she saw the scene behind her. Ward was stood in front, Garrett behind him with a few other guards surrounding them, guns pointed in her direction.

"Put the drive on the side Agent Skye." Garrett told her, his voice an even tone.

She glanced at her partner to see what he wanted her to do. "Do what he says." He told her, his hands behind his back as if they were handcuffed.

She nodded a took a deep breath, nodded and placed it back on the side besides the computer. They'd been caught before, but never by Hydra, she wasn't sure of what they were capable of. She turned back to all the men. "You've got what you wanted, can we go now?" She asked.

"No." Was the simple response.

"Thought not, it was worth a try." She muttered.

Ward got shoved across the room, close to her. "Hey." She whispered and looked up at him. She quickly ran her eyes down his body, checking for injuries. "You hurt?" She asked and he shook his head before reaching for the gun at her side. "Trust me." He whispered to her as he pocketed the gun.

She nodded before turning back to all the Hydra Agents. "So plans for us..?" She started before she felt Ward grab her hands from behind her and she felt cold metal tighten on her skin.

"Ward..Grant..what are you doing." She growled and pulled away from him, pulling on the metal but she knew it was a lost cause. She wasn't going to break them. She watched him carefully as he turned to Garrett, who gave a quiet laugh before Ward turned back to her, a sinister smirk on his face.

"Hail Hydra." He told her.

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 **A/N Dun Dun Duuuuun.**

 **I don't plan on having days when I upload new chapters, it's kinda just be updated when I've wrote a chapter. So sorry about that.**

 **For the guest that said I should add romance, it's a SkyeWard story, so good things come to those who wait ;)**

 **Thanks for the 19 followers, 5 reviewers and the 7 favourites, the notifications have made my last few days :)**


	3. Chapter 3

**A/N**

 **So I couldn't reply to the guest who said they were sick of Hydra!Ward stories, don't worry, I know where this is going sort of and I'm also annoyed of what they did to him on the show, just watch how it plays out ;)**

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"Hail Hydra." He told her.

Skye felt her face fall in confusion. "What? No. Stop playing around Grant. This isn't funny." She whispered as she searched his face for any signs of lies but it was a challenge considering he was the best at espionage since the Black Widow herself. "Why aren't you trying to take any of them out." She asked.

"Because I don't have any reason to." He looked up at Garrett who just nodded. Skye hated that they weren't communicating verbally, they seemed too close. "You're coming with me." He mumbled and grabbed her arm, trying to make it look forceful even though it wasn't. He pushed her gently towards the door as more of a prompt to leave than anything. Skye didn't bother fighting back, it was a lost cause, he taught her everything she knew which wouldn't work to her advantage.

When he knew Garrett couldn't see them anymore from where they were previously, he leaned down close to her ear. "Please play along, I didn't mean for any of this to happen." He whispered and kept hold of her in case she still tried to get away from him. "I can explain all this another day but you really need to keep thinking of me as the bad guy for now." He told her before he pulled away as another Hydra agent walked by them.

"You're a complete ass Grant Ward, this is me being nice in my mind. I'm not even playing along right now." She growled as they reached a rather spacious cell. "You can stay here for all I care. You kept this from me for I don't know how long. In my mind you are the bad guy" She said and turned to him at the door.

Ward swallowed, knowing that she was serious but also hating himself for not being able to explain and try put things right at that moment in time, so he didn't reply to what she said, instead he looked over her shoulder as a distraction. "Coulson has the key to these cuffs. I pulled the screws from the window at the back of the room and he's waiting for you just outside the gates which have been conveniently left unlocked." He said bluntly. "See you later." He muttered before pushing her in and slamming the door. On the cameras it would just look like some kind of argument between the pair, which it partly was, rather than an escape plan.

He only stayed at the door for a few seconds, not enough for anything to get suspicious about, before he went back to Garrett. He knew what was going to happen the moment he tried to return to the Bus and speak to Skye but he pushed it to the back of his mind, he had to stay in character for this to work.

Once back in the room, his stone cold expression back on his face, he approached the man he called a leader. "She's contained but she's not to be talked to by anyone but me and you, you're not to do so much as touch her." He warned him. "I don't care what you think. That was the deal. She hates me but I still have a level of respect for her."

Garrett hit him on the back, like Fitz did sometimes in a brotherly way, but with John it was more him trying to keep control of him. "Of course Ward, but remember that there will be a day where we'll have to do something with her, she'll comply to our ways or she'll end up with a bullet in that pretty little head of hers. That choice will be left to you though." He smirked, Grant clenched his fists and didn't say anything at first.

"Of course, she's an asset. Why do you think I was sent after her along with several other organisations? She's better alive than dead." He shrugged. "Moving on, where am I needed next?" He asked as Garrett moved his head to signal that they take it to his office.

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Skye stood looking at the closed, heavy bolted door that Grant slammed in her face only seconds ago. Angry wasn't the right word to describe her feelings at that moment in time. She had so many questions but she wasn't so sure she even wanted to hear the answers, from him especially. If he had planned a way for her to leave without anyone knowing that would mean he'd either set up the whole mission for this to happen or it had been planned for a while and Coulson was in on it some way.

She shook all the thoughts out of her head for the time being and walked over to the window Ward had told her about, it was the only one in the room so she assumed that's the one he meant. It was difficult to be silent in moving the window when her hands were still cuffed together behind her back but she managed. She sat in front of the window and checked it to be sure he was telling the truth, which he was, before she kicked it hard. The window only dropped about 3 foot which told her she was on the lowest above ground level. She glanced back at the door to make sure it was still locked before she awkwardly made her way out of it.

Once outside she had a quick look around to check for any guards, Ward had probably ordered them to the other side of the building so she could do this, he didn't give her any timings so she guessed he wanted her gone as soon as possible. She started to run but kept as low as she could, not going into any large open spaces. She saw the gates that he had mentioned and ran towards them. She only heard the gunshot a second before she felt a pain in her left side. She pushed through it and ran towards the SUV she knew was Coulson's that was parked under a tree as some sort of cover. Another gunshot was heard and she looked up to see that Coulson was out of the SUV now, gun raised towards the other agent who had shot her.

He ran towards her before helping her into the passenger side of the car and uncuffed one of her hands as they were in a rush before he jogged to his side and started it up, driving away swiftly. "I was meant to cover you, sorry, I didn't see him." Coulson spoke up after a minutes silence when they were back on a proper road. "And I'm sorry about all of this, I guess you've figured out that I knew about Ward, but I can promise you that I found out hours before you left for your mission." He told her, shifting his gaze to look at her.

Skye was holding her side, her shirt bunched up in that area. They'd managed to hit where the vest had ridden up slightly from when she was running. She was tense and showed no signs of replying but her expression showed she was in pain, which he didn't like to see.

"When we get back, Simmons will patch you up and then we can talk about this, Ward told me what I needed to tell you so I guess that's better than nothing." He explained then after that the whole journey was silent.

Once they had pulled up in the cargo hold of the Bus, Coulson walked around and helped her out. Simmons was already waiting for her. Coulson walked her up and sat her down before telling her he'd be in his office for after. He was blanked by her.

Simmons was working on pulling off the vest as best as she could without hurting her and then immediately started to clean the wound, it looked like a flesh wound more than the bullet properly penetrating the skin which she was grateful for. She stitched the wound up carefully and gave some drugs to Skye that Ward had recommended. They numbed the pain but made sure the user was still aware of their surroundings and could fight back if needed.

Skye brushed her offer of helping her up and she made her way up the stairs slowly, the medicine having not kicked in yet meant it still hurt to do anything, including breathe. She started walking towards the staircase that lead towards Coulson's office before quickly turning on her heel and retreating to the cabin Ward had been assigned. This was the closest she could be to him and not be mad. It offered as some kind of comfort.

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 **A/N Sorry for the wait, I just got caught up in a few things.**

 **Thanks for all the reviews, follows and favourites.**

 **Hope you enjoyed!**


	4. Chapter 4

It had been two weeks since she had last talked to Ward and she had ignored Coulson everytime he tried to explain to her what Ward wanted her to know. She had been angry, so angry at Ward but at the same time she'd missed him so much. She hadn't slept in her own room since he'd left as she'd never really left his, it was comforting for her in some way.

Her anger had been a problem though as she had taken her anger out on others, including FitzSimmons which ended up with an immediate apology as she felt bad the minute she snapped. The worst fight she'd gotten into was with May earlier that day. You should never snap at Agent Melinda May. She regretted that. She'd humiliated herself in her mind.

 _"You need to stop moping around and talk to Coulson, he's trying to help." May told her, her voice firm. "We're all sick of seeing you this way and I know I'm being blunt but I think this might be the only way to actually get through to you seeing as you've pretty much offended everyone else on this Bus which is weird considering you're not even a core member on here. We're keeping you here because we consider you one of us so you better start treating us the same way." May had gotten a brief explanation to what was happening from Coulson, nothing much but she knew parts of it._

 _"Thanks for your comforting words but I don't need it." Skye told her and turned around from where she was heading before she was interrupted. "I don't think you realise that he was the closest to family I've ever had and I haven't done so much as heard from him in two weeks. I'm worried for him. So I think it's best you just keep out of it for now." Skye told her and stepped closer to her, trying to seem bigger than she was._

 _"He's on a mission and you need to start taking care of yourself. You've not been socialising properly or even eating with you. You don't seem to understand that some of the members of this team are concerned for you." May told her and stood a little taller, she knew what was coming. She caught Skye's fist before it even came too close to her face. Skye had tried to punch her. "I suggest you go back to yours or Ward's room and take a breather before you do something like that to one of the members that aren't as great at blocking your punches." May warned before she dropped her hand and walked off._

Skye had done what had been recommended and had retreated back to her partner's room and sat on the corner of his bed for the best part of two hours before she was brought back from her daydreams by a knock on the door, followed by Fitz sliding it open, a soft smile on his face. "You might wanna come with me. Coulson found something by the Bus we need you to look at." He smiled and nodded his head in the direction of the hallway.

She frowned slightly and got up, wiping her eyes gently, she hadn't even realised that she had been crying till then. "What is it?" She asked as she followed him out, he didn't reply but still made sure she was close as they descended down the spiral staircase by the lab.

Ward was stood there, cuts on his right cheek and along his hairline, his left eye slightly blackened. He was holding his left side too. She could see he was in pain and was trying to hide it but she could see right through him this time. Coulson was stood to the left of him as he watched Skye carefully. He really didn't need her attacking him in rage when he was like this, not that he'd try stop her once he was fully healed.

She came down the rest of the steps and walked closer till she was stood in front of her, biting her lip in order to stop herself from crying again. He looked terrible. "Ward.." She whispered and looked up at him, her hand coming to rest on the uninjured cheek. "He found out you were really Shield didn't he." She asked quietly and she caught his nod. her face fell slightly and she pulled him into a loose hug so she wouldn't hurt him. "I'm so sorry for hating you." She mumbled against his jacket as her hand held it in a fist.

"You hated me?" He whispered back and held her with one arm.

"You left me. Of course I did." She replied

"I'll make it up to you, you know when I'm not bleeding." He mumbled as she pulled away.

She turned her head to Coulson. "I'm sorry for ignoring you, I was just annoyed at this one." She admitted and pointed towards Coulson. She spotted May on the balcony. "I'm sorry for trying to punch you." She told the older Agent and she just turned away now that she had seen this scene take place.

"You tried to punch her?" Ward asked with a frown, which drew her attention back to him. "I'm guessing because you were angry at me?" He asked and she nodded.

"I'm sorry. Turns out this is why we shouldn't do solo missions without seeing each other." She said with an awkward laugh.

He pulled her closer again and kissed the top of her head. "I won't leave you again. I promise, but right now I want you to patch me up." He whispered to her so Simmons wouldn't hear him. He just wanted to be close to her again.

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 **A/N So it's been a while and it's gone 2Am but I wanted to get this up. More detail in the next update :)**


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